cleanup: Removes unused MARK output files
In RMark: R Code for Mark Analysis

cleanup

R Documentation

Removes unused MARK output files

Description

Identifies all unused (orphaned) mark*.inp, .vcv, .res and .out and .tmp files in the working directory and removes them. The orphaned files are determined by examining all mark objects and lists of mark objects (created by collect.models) to create a list of files in use. All other files are treated as orphans to delete.

Usage

cleanup(lx = NULL, ask = TRUE, prefix = "mark")

Arguments

`lx`	listing of R objects; defaults to list of workspace from calling environment; if NULL it uses ls(envir=parent.frame())
`ask`	if TRUE, prompt whether each file should be removed. Typically will be used with ask=FALSE but default of TRUE may avoid problems
`prefix`	prefix for filename if different than "mark"

Details

This function removes orphaned output files from MARK. This occurs when there are output files in the subdirectory that are not associated with a mark object in the current R session (.Rdata). For example, if you repeat an analysis or set of analyses and store them in the same object then the original set of output files would no longer be linked to an R object and would be orphaned.

As an example, consider the mallard analysis. The first time you run the analysis script in an empty subdirectory it would create 9 sets of MARK output files (mark001.out,.vcv,.res,.inp to mark009.out,.vcv,.res,.inp) and each would be linked to one of the objects in nest.results. When the command AgePpnGrass=nest.results$AgePpnGrass was issued, both of those mark objects were linked to the same set of output files. Now if you were to repeat the above commands and re-run the models and stored the results into nest.results again, it would create files with prefixes 10 to 18. Because that would have replaced nest.results, none of the files numbered 1 to 9 would be linked to an object. cleanup(ask=FALSE) automatically removes those orphan files. If you delete all objects in the R session with the command rm(list=ls(all=TRUE)), then subsequently cleanup(ask=FALSE) will delete all MARK output files because all of them will be orphans. Output files can also become orphans if MARK finishes but for some reason R crashes or you forget to save your session before you exit R. Orphan output files can be re-linked to an R object without re-running MARK by re-running the mark function in R and specifing the filename argument to match the base portion of the orphaned output file (eg "mark067"). It will create all of the necessary R objects and then asks if you want to use the existing file. If you respond affirmatively it will link to the orphaned files.